A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought

Simple item page
dc.contributor.authorMolitor, Corentin
dc.contributor.authorKurowski, Tomasz J.
dc.contributor.authorFidalgo de Almeida, Pedro M.
dc.contributor.authorKevei, Zoltan
dc.contributor.authorSpindlow, Daniel J.
dc.contributor.authorChacko Kaitholil, Steffimol R.
dc.contributor.authorIheanyichi, Justice U.
dc.contributor.authorPrasanna, H. C.
dc.contributor.authorThompson, Andrew J.
dc.contributor.authorMohareb, Fady R.
dc.date.accessioned2024-05-09T12:22:29Z
dc.date.available2024-05-09T12:22:29Z
dc.date.issued2024-03-08
dc.description.abstractIntroduction: Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. Methods: In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads. Results: The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production. Discussion: Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.en_UK
dc.description.sponsorshipThis work was jointly supported by the UK’s Biotechnology and Biological Sciences Research Council and the Indian Department of Biotechnology (BB/L011611/1).en_UK
dc.identifier.citationMolitor C, Kurowski TJ, Fidalgo de Almeida PM, et al., (2024) A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought. Frontiers in Plant Science, Volume 15, March 2024, Article number 1342739en_UK
dc.identifier.issn1664-462X
dc.identifier.urihttps://doi.org/10.3389/fpls.2024.1342739
dc.identifier.urihttps://dspace.lib.cranfield.ac.uk/handle/1826/21588
dc.language.isoen_UKen_UK
dc.publisherFrontiersen_UK
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectGenome assemblyen_UK
dc.subjectS. chilenseen_UK
dc.subjectBUSCOen_UK
dc.subjectdroughten_UK
dc.subjectsalten_UK
dc.subjecttranscriptomeen_UK
dc.titleA chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and droughten_UK
dc.typeArticleen_UK
dcterms.dateAccepted2024-02-12

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Chromosome-level_genome_assembly-2024.pdf
Size:
4.55 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.63 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

Staff publications (SWEE)